even with the toner process and sharpie markers..
I get a pitted PCB or two once in a while. This was attributed to over-etching for me, and I'm positive on this, as under etching did not yield the same results, or anything close. I use heated etchant, in a MG chemicals etching/agitiation tank (the big one)
While making the first set of Koichi transmitters, I had a board or two that were pitted, even using the photo exposure process and not the toner transfer process. I'm almost positive now, that this is an over etching problem in one way or another. It can also relate to the style of toner. Toner is porous by nature (as the TTS paper directions describe) and require a sealing layer of GREEN TRF... also sold by pulsar with their TTS paper. This should ifx the problem, and I Regret not sending some along with the TTS paper.
See if the green TRF will help you, it is made for sealing pitts in toner to prevent your problem you are having
As you can see, My Koichi TX boards, although done by photo exposure, stil have a layer of green coating over the copper.